Fix matplotlib version issues and a circular import issue

[chansigit]

• Upgrade matplotlib from 3.5.3 to 3.7.5 (we can actually move forward to 3.9.0 by abandoning python 3.8 )
• Fix a circular import issue in dym.pp.cell_cycle (this function uses dyn.tl.utils when it is partially imported), I now move imports inside functions group_corr and group_score
• I also removed python 3.7 tests. Python 3.7 is so old and doesn't support matplotlib3.7.5 and other new version scverse packages.

[chansigit]

@Sichao25 Hi, Sichao, I believe a lot of failed tests were attributed to this issue.

Can we find a better way to store the data? It seems that dropbox banned the non-browser downloading?

One possible solution is to use some professional research data sharing platform like figshare (I've uploaded the data here https://figshare.com/articles/dataset/Dynamo_sample_datasets/25690782).

This works

adata=dyn.sample_data.get_adata(url='https://figshare.com/ndownloader/files/47420257', filename='zebrafish.h5ad')

[Sichao25]

@Sichao25 Hi, Sichao, I believe a lot of failed tests were attributed to this issue.

Can we find a better way to store the data? It seems that dropbox banned the non-browser downloading?

One possible solution is to use some professional research data sharing platform like figshare (I've uploaded the data here https://figshare.com/articles/dataset/Dynamo_sample_datasets/25690782).

This works

adata=dyn.sample_data.get_adata(url='https://figshare.com/ndownloader/files/47420257', filename='zebrafish.h5ad')

Sounds great. Thank you for detecting this issue.

[chansigit]

@Sichao25 Hi, Sichao, I believe a lot of failed tests were attributed to this issue.
Can we find a better way to store the data? It seems that dropbox banned the non-browser downloading?
One possible solution is to use some professional research data sharing platform like figshare (I've uploaded the data here https://figshare.com/articles/dataset/Dynamo_sample_datasets/25690782).
This works

adata=dyn.sample_data.get_adata(url='https://figshare.com/ndownloader/files/47420257', filename='zebrafish.h5ad')

Sounds great. Thank you for detecting this issue.

I've already uploaded all dropbox-based data to figshare and changed the urls in the codes in my own branch. Now trying to pass the github action unit tests.

[codecov-commenter]

⚠️ Please install the to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

Attention: Patch coverage is 58.02752% with 183 lines in your changes missing coverage. Please review.

Project coverage is 43.60%. Comparing base (26bc5a5) to head (8d7c134).

Files	Patch %	Lines
dynamo/plot/utils_dynamics.py	0.00%	17 Missing ⚠️
dynamo/plot/scatters.py	25.00%	15 Missing ⚠️
dynamo/estimation/csc/utils_velocity.py	30.76%	9 Missing ⚠️
dynamo/plot/utils.py	35.71%	9 Missing ⚠️
dynamo/tools/pseudotime.py	50.00%	8 Missing ⚠️
dynamo/plot/sctransform.py	30.00%	7 Missing ⚠️
dynamo/shiny/lap.py	53.33%	7 Missing ⚠️
dynamo/tools/moments.py	0.00%	7 Missing ⚠️
dynamo/estimation/tsc/twostep.py	0.00%	6 Missing ⚠️
dynamo/plot/dynamics.py	25.00%	6 Missing ⚠️
... and 46 more

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Additional details and impacted files

@@           Coverage Diff           @@
##           master     #686   +/-   ##
=======================================
  Coverage   43.59%   43.60%           
=======================================
  Files         161      161           
  Lines       28697    28724   +27     
=======================================
+ Hits        12511    12524   +13     
- Misses      16186    16200   +14     

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[Xiaojieqiu]

@chansigit excellent work! can we also support python 3.10 and 3.11, etc?

[Xiaojieqiu]

I have made a few comments

[Xiaojieqiu]

can we add 3.9, 3.10, 3.11, 3.12?

[chansigit]

3.12 failed due to the removal of distutils package https://stackoverflow.com/questions/77247893/modulenotfounderror-no-module-named-distutils-in-python-3-12

other versions on the way

[chansigit]

3.10 and 3.11 also failed. we need more time to get it pass.
I noticed scanpy is asking a python version <3.10, we may remain in 3.9 temporarily.
https://github.com/scverse/scanpy/blob/db2118e8eb60bbf6287ce1413477480e16b2508b/pyproject.toml#L70

[Xiaojieqiu]

@Sichao25 can you please reviewer it and finalize it? I will merge it to the main branch later

[Sichao25]

Looks good to me!